#! /usr/bin/env bash
###
 # @Descripttion: 
 # @version: 
 # @Author: Yang jin
 # @Date: 2021-09-07 09:33:46
 # @LastEditors: Yang jin
 # @LastEditTime: 2022-02-16 14:35:02
### 

#fprintf(stderr, "Usage: ./fast-fasta2kmers <in.fa.gz> <out.fa> <mode> <k>(mode:0 non-overlapping fragment;1 overlapping kmers;2：nonoverlapping kmer; 3: variable overlapping kmers;4:overlapping pair kmers;5:non-overlap pair kmers)\n");

# ./fasta2kmers /workspace/datasets/cds/homo/non-human/val.fna /workspace/datasets/cds/homo/non-human/val.fna.500.fragment 0 500
# 模式为2:切割为单条的（unpair）不重叠kmers;模式为5 :切割为成对的（pair）重叠kmers;


#模式7：fragment length=500 stride =100，并去掉长度不大于250的fragment
# ./fasta2kmers /workspace/CAMI-contigs/cami-high/gsa_596.fa /workspace/CAMI-contigs/cami-high/gsa_596.fa.500.100str 7 500 100     

# #模式1 切割为 stride =1 的6mer
# ./fasta2kmers /workspace/CAMI-contigs/cami-high/gsa_596.fa.500.100str /workspace/CAMI-contigs/cami-high/gsa_596.fa.500.100str.6mer 1 6       



# ./fasta2kmers /workspace/CAMI-contigs/cami-low/gsa_40.fa /workspace/CAMI-contigs/cami-low/gsa_40.fa.500.100str 7 500 100     

# #模式1 切割为 stride =1 的6mer
# ./fasta2kmers /workspace/CAMI-contigs/cami-low/gsa_40.fa.500.100str /workspace/CAMI-contigs/cami-low/gsa_40.fa.500.100str.6mer 1 6       

# ./fasta2kmers /workspace/mother/megahit/4-contigs.fa /workspace/mother/megahit/4-contigs.fa.500.frag 0 500    

#模式1 切割为 stride =1 的6mer
./fasta2kmers /workspace/vamb-data/airways/contigs.fa.500.frag /workspace/vamb-data/airways/contigs.fa.500.frag.4mer 1 4      

